The Fallen Leaf
by Thatoneguy1109
Summary: What if Pein kept true to his promise of destroying Konoha? What would have happened if Naruto was unable to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic. OOC Characters (especially Naruto)
1. Vengeance

What if Pein kept true to his promise of destroying Konoha? What if Naruto was to late to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic.

* * *

 **i do not own nor do i claim to have any rights to Naruto. All rights are reserved to its author Masashi Kishimoto.**

* * *

"It was never supposed to come to this. This was never supposed to happen."

"When the toads told my sensei that one of his students will bring about a great change to the world, i never would have expected this to be the change they spoke of."

"Yet again, maybe i shouldn't have expected anything less. After all, isn't this why their prophecies are always so fucking vague."

"Nevertheless, they weren't wrong. A change did occur. And one of his students did cause it."

"Funnily enough, it wasn't even the student that was already hell bent on world domination."

"No he is long dead by now."

"What happened to him? Simple, I killed him."

"He was the first of many deaths that bring me here to where it all began."

"Where things changed forever."

"And so here I am on the remnants of the Hokage monument staring at the crater filled with ashes and dust of the village that used to be konohagakure no soto."

"I can still remember the faces of the countless people that died here. Shinobi and civilians, old and young…friends and loved ones."

"All slaughtered because of the insatiable monster that is human greed and desire."

"Though those responsible of this atrocity aren't completely at fault for the state that the world is currently in. No, there is one monster far more destructive than greed and desire."

"Vengeance."

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."

"Such a nasty thing it is. Saw its effects first hand many years ago. How it left a hole in his heart and sent him on a path of self-destruction. Yet still i remained ignorant to it."

"But now, I think I finally see what he meant. Funny how i can relate to him in more ways than he can imagine."

"Enough about my past. I was blind then. Foolish enough to believe that peace can be obtained in this world. That humans can understand and forgive one another."

"Not anymore. My eyes have finally been open. Unfortunately, i had to die in order to see."

"My name is Naruto Uzumaki. The last of the loyal shinobis that belonged to the village hidden in the leaves."

"This is my story."

"My vendetta against those who wronged me."

"My death."

"And how the Demon of the Fallen Leaf was born."

* * *

 **Hey guys. Thatoneguy here. This is an idea that I've had for quite some time. As stated above, this is my first shot at a fanfic. I've yet to see a story where konoha fell after the Pein Invasion so I'm kinda just hoping that people read this intro and get somewhat inspired to create their own. Im not much of a writer and the only experience i have is my high school english class. i don't really have a plan for this story or even an idea to where its heading and how to get there. More like key plots and events i want to happen. I don't really intend to follow canon after the pein invasion and i might change a couple of key events before the invasion. So expect updates to be slow, if not non existent. After all, I'm much more of a reader than a writer and i suck at creating original ideas.**

 **Anywho hope this idea intrigues you as much as it did me. Till next time.**


	2. Retaliation

What if Pein kept true to his promise of destroying Konoha? What if Naruto was to late to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic. OOC characters (especially Naruto)

* * *

 **i do not own nor do i claim to have any rights to Naruto. All rights are reserved to its author Masashi Kishimoto.**

* * *

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming." -Speech

 **"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."** -Bijuu or other entity speaking

 _ **"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."**_ -Bijuu or other entity thinking

 _"_ _Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_ -Thoughts

 **Taijuu Kage Bunshin no Jutsu-** Justus or other techniques

* * *

 **AN**

 **Hey guys. I'm back again with another chapter. Honestly, i didn't expect to be writing one so soon. Im having difficulties trying to come up with ways so my story heads in the direction i want it to go, without making it seem forced or unbelievable. My respects to those authors who can create their own arc and still be able to smoothly blend it in with the existing naruto universe. Anywho, i will sorta be writing my first fight scene in this chapter. I apologies in advance if its underwhelming or just plain boring. I promise i will do my best to get better, or if not, i'll look for someone who actually knows what they're doing to write them for me. This chapter also marks the point in time where my story will somewhat begin to diverge from canon. i will still use some arcs from the canon but expect them to be different as well.**

* * *

 _"_ _I cant let anything happen to her. I cant let her get harmed any further for me."_

These were the thoughts of Naruto as he tried to enter sage mode. Usually, doing so would be a breeze for him. But he was having troubles due to the sound of Hinata's yells of pain as she so desperately tried to free him from the chakra rods that pein had carefully impaled him with.

That thought brought him back to his current predicament. Naruto was currently lying flat on the ground with various black chakra rods sticking out from his body, and one impaling his arms to the ground. The rest of the rods weren't embedded deep. In fact, their shallowness wouldn't actually hinder his movement too much. If he could activate sage mode, his pain tolerance would skyrocket enough to allow him to continue the fight. But the rods had Pein's chakra coursing through them. Aside from controlling his movement, the chakra was disrupting his own chakra flow enough to keep him from reaching the balance of nature and regular chakra required to enter sage mode. Maybe if he could remove a couple, the disturbance wouldn't be large enough to distract him, but with his hands rendered useless, there wasn't much he could do. Things weren't looking good for him until Hinata stepped in and managed to break some of the rods.

* * *

 ** _Meanwhile, with Hinata_**

Hinata wiped some blood from her mouth. She had managed to break off a couple of the rods that were damaging Naruto before a **shinra tensei** sent her flying away. Through her byakugan, she could see that the spikes were no longer hindering his ability to enter sage mode. She could visually see the natural chakra gathering around him.

 _"_ _I have to buy him a couple more minutes."_

Hinata sent forth her strike only to have Pein duck underneath it. She brought her other hand forward but he merely sidestepped it while remaining crouched. She attempted to kick him but he jumped over her, landing behind her. She swung her arm while twisting her body in a 180 degree arc to strike him but pein just bent forward and allowed the strike to pass over him before jumping away to avoid a blow where his head used to be.

 _"_ _Just a little bit longer."_

Hinata concentrated chakra into her hands and resumed her assault on Pein.

* * *

Despite not having the visual link from the other rinnegans, Pein had no trouble dodging Hinata's relentless attack. It was obvious that he was merely toying with her.

But enough was enough. He had waited a long time to capture the nine tails jinchuriki and he wasn't going to let this girl halt his progress any longer. It was time he retaliated.

Pein ducked under a strike aimed towards his arm and directed his own towards her torso. Hinata avoided with a quick step back but Pein wasn't going to let her go that easily. With a simple **shinra tensei** , he pulled her back before delivering a strong kick to her side. Hinata barely had enough time to block the kick with her forearms before the force of the strike sent her flying a couple feet in the opposite direction.

Pein immediately capitalized on her momentary stun by sending a punch towards her stomach followed by a knee to her gut with his left leg. Hinata doubled over in pain,and with a swift leg sweep, she was on her back. With no time to react, she rolled away from pein's legs where mere moments later, a chakra rod was imbedded into the ground.

Breaking off the top portion of the rod, Pein sent the jagged metal spike flying towards the overwhelmed girl.

* * *

 _"_ _Done!"_

Naruto raised his head just in time to see the black projectile hit its target and hearing the loud thud that Hinata's body made after hitting the floor.

In that very moment, he saw red.

* * *

"I'm afraid I can't allow you to interfere any longer. This is your end."

With those words, Pein withdrew another chakra rod, intending to end the young girl's life.

But before he could follow through with it, he felt a strong force explode behind him. He quickly turned around to gauge the new threat.

There behind him stood Naruto with his sage mode activated. However this one had a couple key differences from what he had previously demonstrated. Amongst those differences was the thin, but still noticeable chakra cloud, the sharpened canines, the defined whisker marks, and the cross shaped pupils he had.

"You touch her again, and i will rip those god damned eyes from your fucking skull!"

"It seems you don't know when to quit. So be it, it looks as if i'll have to use more force this time."

With that, Pein sent the kyuubified Naruto flying well out of the village with a **shinra tensei**.

* * *

 **AN**

 **I know this chapter was really short. I apologies for that. i promise i'll begin to write longer and longer chapters. i just need to get into the hang of things. I also wanted to just get this part of the fight,if you can call it that, over with. With the way i plan on leading the story, i cant use the regular fight scene that occurred when the kyuubified Naruto went bat shit on Pein, or even have the same circumstances that led to him escaping his predicament. Since Naruto isn't in full kyuubi mode, he will still be in control of his body, but he will be slightly more impulsive. Because of this, I'm going to have to create an entirely new fight scene for the battle between Pein and Naruto Outside of Konoha.**

 **Please let me know what you think of the fight scenes. Either more details, less details, more action, that sort of thing. I know this little scuffle can barely be called a fight but any ideas or feedbacks will be helpful in creating a better fight scene for next time or realizing that I'm a lost cause when it comes to battles and that i should find a suitable writer for all of my future skirmishes.**

 **Anywho, i'd like to thank Crescent-Moon0Sesshomaru, Illuminated, and RoyaN G J for following my story. Special shout-out to Crescent-Moon0Sesshomaru for being my first reviewer. Your comment really made me want to write again and just plainly made my first post enjoyable. I never really understood why authors always want reviews until now. Just a simple, "Good Work" makes the entire effort in writing a story so rewarding. Just know that the only reason i continued writing was because of your comment. I'll try not to disappoint you bud.**

 **Anywho its 3:00 in the morning so I'm going to post this real quick and head to bed.**

 **Till next time!**


	3. Confrontation

What if Pein kept true to his promise of destroying Konoha? What if Naruto was too late to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic. OOC characters (especially Naruto)

* * *

 **I do not own nor do I claim to have any rights to Naruto. All rights are reserved to its author Masashi Kishimoto.**

* * *

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming." -Speech

 _"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_ -Thoughts

 **"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."** -Bijuu or other entity speaking

 ** _"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_** -Bijuu or other entity thinking

 **Taijuu Kage Bunshin no Jutsu-** Justus or other techniques

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."- Flashback

* * *

 **QNA**

 **Illuminated: I do agree that a kyuubified/sage mode naruto would definitely be able to withstand a regular, even an amped Shinra Tensei, though I think if caught off guard, or not prepared, he would still be pushed back by it. Thanks for pointing out that mistake on my part, though. I'll try to elaborate more to avoid confusion.**

* * *

 **Outskirts of Konoha**

Naruto was sent hurtling to the village boundaries with an astounding amount of force, landing face down on the edge of a lake. Had he not been in sage mode, he would have guessed that there would be severe damage done to his body about now. Speaking of which, he looked at his hands to see the extent of damage that Peins acupuncture did. Imagine his surprise to see the holes in his body almost completely sealed.

 _"What!? Sage mode doesn't have any healing propert-"_

Before he could finish his thought, there in the lake he saw the thin, almost feint, demonic chakra encasing his body.

 _"Kyuubi!"_

"I see it was too much to hope that that attack would have taken you out."

Immediately, Naruto's head shot up. There standing across the lake was Pein. Seeing the cause of his afflictions standing before him, he was quickly overcome with an almost primal rage.

"I see you now understand a little more about pain. Maybe now you can begin to see how futile and pointless Jiraiya's views are

"You fucking bastard! I'll kill you!"

With that, Naruto started sprinting towards the stoic man.

Pein leaped into the air and away from where he was previously standing.

 _"Fast!"_

There was naruto with his fist in a crater where rock used to be.

 _"I can't let him strike me. A punch like that will destroy this body."_

Upon landing, Pein shifted his body to the left to avoid a swipe from Naruto's right hand and delivered a quick hit to his oncoming left hand to deflect the hand away. Naruto followed with a kick to Peins midsection. Capitalizing on the stretched appendage, Pein grabbed Naruto's leg and used it as leverage to fling him away.

Pein glanced at his clothing to see slash marks from Naruto's sharpened fingernails. Looking at the torn fabric, he was reminded of the previous battle within the village.

 _"So his sage abilities extend his attack field. Despite missing, he still managed to damage me. That chakra cloak around him will serve as a good indication as to how much his reach extends."_

Using the momentum of the throw, Naruto corrected himself to land on his feet.

 **"Bansho ten'in!"**

Before he could even get his bearings, Naruto was forcefully pulled towards Pein. With a swift kick, Pein sent Naruto flying through multiple trees.

A couple moments passed and Naruto seemed to not be moving. Suddenly, Pein was forced to react to the oncoming projectile.

 **"Shinra Tensei!"**

The repelling force was enough to completely stop the tree that was hurled in his direction. Immediately behind the tree was Naruto with an outstretched fist. Pein evaded the punch and withdrew a chakra rod, managing to graze Naruto's shoulder.

"ARGH!"

Crossing his arms in a protective manner, Pein rode the unexpected shockwave caused by a chakra explosion.

" ** _Kill, maim, hurt him for what he's done."_**

From the dust emerged Naruto in his two-tailed state along with his sage mode.

"It seems you've begun to take this fight seriously."

"Shut up."

"I see the beast has yet to emerge."

 ** _"Kill, maim, hurt!"_**

The voice rang within Naruto's head.

"I said shut up!"

Once more, naruto continued his attack.

* * *

 **Back in the Village**

"Sir!"

Shikaku Nara turned around to see a numerous number of ANBU captains kneeling before him.

"Whats the meaning of this?"

The ANBU Captain upfront answered.

"The Hokage has been incapacitated for the moment. As per the chain of command, you are temporarily the village leader we were ordered to follow during times where martial law is necessary."

"Lady Tsunade?! What happened?"

"The Hokage has been rendered unconscious due to chakra exertion."

"I see. In that case, Status report!"

"We've manage to set up a temporary base of operations near the remnants of the Hokage tower. All personnel have been notified to rendezvous at this location. Our medics are working to treat the injured. The civilians inside the safe zone appear to be unharmed."

"And our forces?"

"It seems that our military strength has been reduced to less than half with most of our forces assumed KIA due to the last attack, and the rest are shinobi that were away from the village during the attack."

"Hawk!"

"Yes, Sir!"

"Initiate Emergency Protocol 12! We must have all shinobi, that are not in missions of top priority, return to the Village at once!"

"Immediately, Sir!"

The ANBU, along with his squad vanished in a shunshin.

"And what of the Akatsuki?"

"Our Hyuuga members tell us that Naruto and Pein have engaged in battle well outside of the village boundaries. But it appears that Naruto has begun using the Kyuubi's chakra. He is currently at four tails and still rising. He appears to be losing control very quickly sir. His attacks have become more feral and unrefined."

"Call back team Yamato. If Naruto loses control, we may need him."

Shikaku turned to see that the words came from Inochi, who had brought along with him a couple other TI members.

Looking back at Shikaku, the ANBU asked hesitantly.

"Sir?"

"Do it."

"At once!"

"Inochi, tell me something good."

"Before the attack commenced, some of the members of Research and Development managed to discover something interesting about the rinnegan wielding members from the body that Lord Jiraiya brought us. It seems that the strange piercings all over their bodies are chakra receiving rods. They act as a conduit for chakra to the reach the bodies from a remote location."

"If that's so, then that means they're merely puppets."

"Precisely, and the real members are somewhere close by. Possibly on some high ground near the village."

"Cat! Assemble a team to find exactly where that signal is located. As for the rest of you, I want a perimeter around our BOA (base of operations) and teams out searching for any survivors."

"Yes Sir!", shouted the captains in unison.

* * *

 **Back with Naruto**

The fight had escalated further. Naruto was quickly advancing through the stages of Kyuubi mode. He was currently in the process of sprouting his 5th tail. Despite that, what little sage chakra he had left still kept the fox from completely overtaking his body, albeit barely.

Pein, on the other hand, wasn't fairing too well either. Despite Naruto's feral behavior, he'd still manage to get a couple hits on him. One particular strike managed to destroy one of the chakra receivers on his left hand, limiting the motion and reaction of the appendage. A quick repair is simple but Naruto hadn't let up on his relentless attack until now. Without hesitation, Pein stabbed the location of the absent chakra rod and broke off the tip to make a makeshift replacement.

 _"I'm going to need to bring him closer to my location in order to capture him if he continues to use the bijuu's chakra."_

"I grow tired of our confrontation. You have the attributes of a beast but still lack its ferocity. Come and attack me, let us finish this."

With that, Pein sent a barrage of chakra rods towards Naruto from above. Naruto swatted them away, momentarily losing site of Pein. Out of nowhere, a chakra rod was embedded into his leg, and he was punched several feet away with a strong uppercut. And with that, Pein vanished, presumably to prepare for the 6th tail that was beginning to form. Naruto ripped the rod out and kneeled onto all four, shouting in pain while doing so.

 ** _"Allow me to end this. I can end your suffering."_**

 _"…"_

 ** _"I can end this quickly. All you need to do is release the remaining sage chakra, and give me control."_**

Upon hearing those words, Naruto's mind brought him back to a memory that occurred a while back during his training.

* * *

 **Flashback**

"What if I hurt you? I can't risk hurting the people I care about in exchange for the fox's chakra. You know I can't control myself when I do. "

"I know you'll never hurt me because I know you won't ever let it control you again. Promise me that you will always stay the way you are. Promise me you'll never change."

Naruto looked up to see nothing but Love coming from her gaze.

"I believe you'll one day achieve that peace you're always yelling about. I know you'll make Hokage, and I'll be by your side when you do."

With those words, Naruto felt a warmth radiate throughout his body. Getting up he gave her a million watt smile.

"Believe it!"

 **End of Flashback**

* * *

 **Present Time**

"…no…"

 ** _"Foolish vessel, remember the pain he's caused. You NEED me!"_**

"I said NO. Never again fox. I won't allow you to hurt any more people because of my recklessness. Now go back to sleep or something."

 ** _"Hm. you know nothing human, you will call upon my power again. Just wait and see."_**

The cloak around Naruto began to fade. He felt numbness from the now closed wound of where the rod used to be. Too distracted, he didn't notice the slight glow that his necklace emanated before it went back to normal.

 _"Damn my sage mode is almost out. I need to find Pein and end this quickly. I may be able to replenish some while I take a breather and locate him."_

Mere seconds passed before naruto had to break his concentration to avoid a lone chakra rod from impaling him.

"So the beast is gone. Good, but I'm afraid I can't let you resupply. Capturing you has already taken far too long"

 _"Damn! Not enough time. I may have a sufficient amount for one rasenshuriken but that's about it."_

Naruto evaded the rod that Pein had attempted to stab him with and grabbed him by the wrist with his left hand while delivering a quick jab with his right. Using the wrist as leverage, Naruto brought Pein closer to the ground to deliver a jumping knee kick to the side of his head.

" _His left hand is much slower than it used to be. But why? Why now?"_

"Naruto-sama."

"Huh!?"

Within his coat, Naruto felt a shuffle before a small slug emerged from the depths of his sweater.

"Katsuyu!"

"Yes, Naruto-sama. I'm still here, and I have new information about the Peins. It seems that their bodies won't be able to function properly without those piercings. The real Pein is somewhere near the village."

" _So that's why he stabbed himself earlier. His arm was failing him, but in my rage, i failed to notice. Damn it!"_

Naruto ended his current train of thoughts to focus on the recovering Pein before him.

"Thanks, Katsuyu!"

"Of course."

The small summon retreated back into the confines of Naruto's tattered sweater.

" _So it seems he's figured it out. I can't give him the chance to capitalize on it. Good thing he only has enough chakra for only one of that nasty wind jutsu."_

Two clones popped into existence next to Naruto and began forming a **rasenshuriken**. Upon completion, the two clones dropped a couple of smoke bombs.

Pein easily deflected the kunai that emerged from the smoke.

 _"As if a god couldn't handle something as mundane as a couple of kunai."_

Immediately following the kunai, the rasenshuriken sliced through the air, aimed at Pein with deadly precision.

 _"How childish."_

Pein sprinted towards the projectile.

 **"Shinra Tensei!"**

The **rasenshuriken** was dismantled quickly.

"How fooli- What!"

 **POP!**

Rather than a dissipation of chakra, the projectile exploded into a plume of smoke that was closely followed by another **rasenshuriken**. With no time to react and nowhere to go, Pein quickly summoned a rod and buried into the ground, using it as a pole-vault to dodge the explosion that occurred behind him.

 _"Two more second left."_

In the air, Pein saw Naruto flying towards him with a **Rasengan** in hand.

 _"One."_

"Almost there."

" **Shinra Tensei!"**

The repelling force sent Naruto crashing to the ground. He struggled to get up before he was lifted from the neck by the ever unemotional rinnegan user.

"It's over."

Pein released a chakra rod and aimed it to Naruto's limbs. Naruto was barely able to grab Peins hand to keep it from puncturing his skin.

"Stop resisting. Let your sacrifice bring peace to the world."

"Give up… on me… giving up."

"So be it."

"AAUGH!"

Without mercy or hesitation, Pein once again impaled Naruto with the chakra receivers.

Moments passed and the Naruto on the ground poofed out of existence.

"What!"

Out of the ground emerged the real Naruto with a **rasengan** in hand.

Before Pein could counter, Naruto struck him down.

"RASENGAN!"

"GYAGH"

A huffing and puffing Naruto stared at the downed form of the self-proclaimed god.

"Now… its over."

* * *

 **AN**

 **Whats up guys. Thatoneguy here. Sorry for the long wait. I got caught up in school, had to handle some drama at home, and I got kind lazy. But I doubt you want to hear my excuses so let's move on.**

 **I stopped here because… well, i don't really have a reason, it just seemed like a good place to stop.**

 **I've included a pairing for the story. I purposefully left her description vague so as to not give away who she may be. I'll try not to give too many hints because I want her to remain a secret. Feel free to guess her identity, cookies for the reader that manages to do so. Just remember that this is an alternate universe so don't discount anybody. I do plan on revealing her identity, but not until much, much later in the story, if not at the very end. Or maybe I'll just let her remain a secret and let you as the reader just imagine whomever you want.**

 **I hope that the fight wasn't a complete disappointment. Like I said earlier, I'm no good at writing fights. I had to rewatch the Konoha invasion arc along with multiple taijutsu fights from naruto and other anime. I even had to read a rather long article I found on google to learn how to write a fight scene. Even so, I feel like I still have a really, REALLY long way to go before I can comfortably write a decent fight.**

 **Anywho, this is the longest chapter that I've done yet, and unlike the other 2, this one isn't mostly authors notes and disclaimers. Hooray!**

 **But seriously, ill continue to work on chapter length. Just let me get used to letting my creative juices flow… that came out wrong.**

 **if you so desire, please leave a review (oh no, I've become just like all the other authors). They really motivate me to get another chapter out quicker.**

 **Shout out to that guest review and Illuminated (i really appreciate the feedback) as well as StoryArk, songohan912, and xASSASSINx140 for following this story, as well as Rinky1991 for adding it to his favorites. Hope I don't disappoint guys.**

 **Till next time!**


	4. Revelation

What if Pein kept true to his promise of destroying Konoha? What if Naruto was to late to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic. OOC characters (especially Naruto)

* * *

 **i do not own nor do i claim to have any rights to Naruto. All rights are reserved to its author Masashi Kishimoto.**

* * *

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming." -Speech

 _"_ _Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_ -Thoughts

 **"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."** -Bijuu or other entity speaking

 ** _"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_** -Bijuu or other entity thinking

 **Taijuu Kage Bunshin no Jutsu-** Justus or other techniques

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."- Flashback

* * *

 **QNA**

 **None**

* * *

Naruto looked down at the unmoving form of the Deva path. He felt fatigue invade his body but ignored it. He had one more enemy to deal with. Looking back at the destruction and devastation their battle caused had reminded him of the state of the village.

 _"_ _How. How did one of your students become like he did, Pervy Sage. How did he lose sight of your dreams."_

The weary shinobi felt a sigh escape his lips.

 _"_ _Only one way to find out."_

Naruto began to remove all of the chakra rods from Pein's body, taking his time to make sure that he hadn't missed any.

 _"_ _Don't want him coming back."_

Upon removing the last one, he took a curious glance at the small black object in his hand.

 _"_ _So this thing is what receives the signal from Pein. A signal can work both ways."_

With that thought, he stabbed his palm just enough to feel the chakra move and flow within him. Using a small amount of nature chakra, he managed to trace the "signal" back to its user.

 _"_ _There!"_

* * *

 **With Nagato**

A pale and sickly looking man with faded red hair opened his eyes. He was situated upon a large contraption. His sudden movement managed to capture the attention of the other individual in the room.

"Whats wrong, Nagato?"

The soft, almost serene sound came from a blue hared woman wearing the signature Akatsuki cloak and an origami flower upon her shoulder length hair. Her orange orbs gazed at the now identified man.

"Deva Path… has been defeated."

The words left her shocked, but her expression did not reveal it.

"What should we do?"

"The nine-tailed jichuriki seems to be heading directly towards us. We will capture him here."

"Very well." she said as she prepared for their visitor, concealing a lone chakra rod in her sleeve. Nagato had given it to her to restrain the jinchuriki if the opportunity presented itself doubt had plagued her mind in regards to whether or not she'd actually use it but it seems she will after all.

As if to hear her thoughts, Nagato called out to her.

"Konan."

She half turned to listen to what her long time friend had to say to her.

"Yes?"

"Should he attack, don't interfere."

* * *

 **Scene Switch**

Just a while away stood Naruto gathering enough chakra to reenter Sage mode.

 _"_ _Im so glad this doesn't have a limit."_

Despite his condition, he felt the calming energy rejuvenating his tired body. Fatigue quickly left his mind as he focused on the deceptionaly fake tree just up ahead. Thoughts of anger and rage briefly filled his mind but he quickly dispatched that train of thought.

 _"_ _Not this time. Not now. I need answers."_

With that he made his way towards the final Pein.

* * *

 **Back in the Village**

"Sir, it appears that Naruto has stopped using the Kyuubi's chakra and managed to defeat the final Pein. According to our Hugas, he is currently heading northeast. We believe he has located the true Pein."

"Call back Cat's squad. I want a team ready to assist Naruto should things take a turn for the worst."

"Yes Sir!"

The ANBU left hastily to complete his task.

Shikaku turned to face the captain of Intelligence Division.

"Inochi, I want you on that team. If the opportunity to capture the leader of the Akatsuki presents itself, do so.

"Hai."

* * *

 **Back with Naruto**

Staring at the thick folds of paper that made up the trunk of the "tree," Naruto couldn't help but feel dread for the upcoming confrontation. These are the people who killed Jiraiya and Kakashi-sensei. Who destroyed his village and murdered countless innocent people. Jiraiya's teachings flashed through his mind, but did little to dissuade his rage at them. With sage mode active, he could feel their presence on the other side, further angering him in the process.

With little effort he tore through the paper and made his way inside. Standing on the other side was Pein.

* * *

 **Inside**

Konan made a swift motion to position herself in-between the two.

"Konan" commanded Pein, as if correcting a small child.

The simple call of her name was enough for her to know what Pein meant. She stepped aside albeit with unseen reluctance.

"So you're Pein."asked Naruto

"That I am, and i must say you've proven to be more trouble than I anticipated."

Naruto's eyes were shadowed by his hair. He could feel himself trembling at the thought of all this man has done.

The tension in the room was thick, and Pein was not blind to the anger the was rising within the blond before of him.

"Killing me will not change anything. It will only be for you're own personal satisfaction."

Naruto made no move to respond.

"Your role is to be the catalyst through which i shall bring true peace!"

In an instant, a panel opened in front of the machine Pein was upon, and a chakra rod was launched towards Naruto.

* * *

 _(Drip, Drip, Drip,)_

The rhythmic splashing of Naruto's blood was all that could be heard within the tree. Naruto fell to his knees as Konan moved between the two, incase the jinchuriki had something up his sleeve.

"At this range, I can control you with my chakra. Don't worry. I didn't hit any vital spots. We still need you."

Despite the dire situation, Naruto refused to look up at the man before him, opting to instead talk to Pein as he is.

"H…How?" asked Naruto in a calm, yet serious voice.

"What do you mean?"

Naruto's breath was shaky. His tone rising to a yell.

"How did you, a student of Jiraiya-sensei become like this? Don't you remember what he worked his whole life for? Don't you care that you are doing the opposite of what he taught us!"

Pein remained impassive at his tone.

"Jiraiya's teachings were the ramblings of a man blinded to the truth. Even now, I can see the hatred within you."

Naruto's yell subside, and he responded in a defeated manner.

"You're right."

Naruto raised his head, his eyes still possessing the traits of sage mode. His body trembling.

"Even now, i want to kill you so badly! I can't help but want to make you pay!", he screamed.

Naruto took his eyes off of Pein, choosing to look at the ground instead.

"But I can't."

Naruto's eyes began to water as tears made their way down his face.

"All my life, I've been hated. I've never had a family, and never knew what its like to be loved until recently. I should hate the world and you especially for taking my precious people."

Naruto's eyes quickly regained focus, losing the tears that were welling up in them.

"But someone has to break that cycle of hatred. Sensei's teachings may not have been perfect, but they weren't wrong."

Pein merely stared at the ninja in front of him before answering.

"Perhaps in a world without shinobi, his words may hold merit. But this world is full of killers. No man, woman nor child wearing a headband is innocent of death. So long as shinobi exist, man will always have blood on their hands."

Defiant as ever, Naruto retorted.

"People can change. I'm proof that things don't have to be like this."

"Proof? You're merely blind to pain, and the reality of this world. There's only so much a man can lose before forgiveness becomes a meaningless word."replied Pein. "You preach of proof yet i can still sense your hatred of me. You haven't changed, and neither will this world… Not without a reason for it to do so."

"Peace through fear is no peace at all!"

"It matters not what you think. Your capture has been postponed far enough. Konan."

Konan made her way behind Naruto preparing her jutsu to encase Naruto in paper, and leave him completely vulnerable.

* * *

 **In Naruto's Mind**

Now normally, the fox wouldn't have any means of knowing whats happening outside of the seal, but thanks to Naruto's overuse of the kyubi's chakra, the natural weakening of the Eight Trigram seal holding back the demon fox had been accelerated enough to allow him access to Naruto's senses.

The moment he saw his container get impaled by those God forsaken rods, he began to pump as much chakra as he could into the seal in order to break the rinnegan wielders control, but alas, it still remained strong. The seal had still not been weakened nearly enough to allow him such ability.

However, being a being that has lived for centuries had its perks. The fox knew that the seal only worked because it restrained only half of his chakra, his yang half to be precise. A stronger seal, one much like that of his previous container, would be needed to contain the full power of the nine tailed demon fox. So over the course of his imprisonment, he had been gathering ying chakra to aid in his escape when the seal was weakened enough.

But desperate times call for desperate measures, and he will not be extracted just to be used as some mindless weapon.

 **"** **I will not be captured here you insolent worm!"**

With a deafening roar, the Kyubi released enough chakra to bypass the seal.

* * *

 **Outside**

Naruto could feel the turmoil within his subconscious, and knew that the fox was up to something. His gaze caught glimpse of a metallic object in Konan's sleeve. Quickly, he formulated a plan, and spoke to Pein once more.

"So this is it? There is no changing your mind?"

"I'm afraid not", replied Pein after a short pause.

As if to accept his fate, Naruto looked down once more, before silently murmuring one final sentence.

"Then I'm sorry."

Without sign or warning, Naruto's chakra exploded into a crimson cloak unlike any he has felt before. Without missing a beat, he capitalized on the distraction and turned around to take the object he spotted earlier, before punching Konan hard enough to send her flying back quite a distance. Knowing that attack wont keep her down for long, Naruto set his eyes on Pein.

* * *

 **With Nagato**

The entire ordeal was over before Nagato even knew what had happened. One moment he was restraining the kyubi jinchuriki, and the next, the konoha nin was looking directly at his eyes. He never felt the pain of the rod impaling his liver, nor the sound of multiple konoha shinobi entering the tree. He just peered into his killers eyes.

But rather than seeing victory or even contempt for killing the one who destroyed his village, Nagato saw something else. He saw the look of a defeated man. One who had lost everything and had finally seen the world for what it truly is. A look he was entirely to familiar with as it was the same look he had when Yahiko had died in front of him.

Nagato could feel his body growing colder. Lacking the strength to keep himself upright, he rested his head on Naruto's shoulder, parting some final words to the blond.

"Now… You know Pain."

With that, Nagato Uzumaki died.

* * *

 **Hey guys. Still alive and kickin.**

 **Once more, I'm sorry for the short chapter (didn't make much progress on working on that annoying flaw), and especially for the really, really late update. To be fair, i did say they were going to be slow, but even i think that 9 months is pushing it.**

 **i wont go too much into details because i doubt you wanna hear it, but for those of you who must know, i was having trouble writing this chapter, and was constantly busy with school and graduation, and then i just lost interest in everything related to fanfiction. But good news is I started reading fanfic again a couple days ago, and that made me want to write once more.**

 **I really, really wanted to continue writing this chapter, but i felt it was necessary to stop here. I wish i could of made the chapter longer too, but I'm a crappy writer. But worry not, I'm working on the next update as soon as i post this. Im still pumping with the sudden excitement of writing so i better use it while its there.**

 **So what do you think is the reason Naruto is experiencing what he is feeling at the moment? Well if you're lucky, you wont have to wait too long to find out. The next chapter will be tricky to write, but i'll eventually get it out.**

 **Anywho, till next time.**


	5. Pain

What if Pein kept true to his promise of destroying Konoha? What if Naruto was to late to save everybody? What if the Village Hidden in the Leaves fell on that day? AU. First fanfic. OOC characters (especially Naruto)

* * *

 **i do not own nor do i claim to have any rights to Naruto. All rights are reserved to its author Masashi Kishimoto.**

* * *

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming." -Speech

 _"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_ -Thoughts

 **"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."** -Bijuu or other entity speaking

 ** _"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."_** -Bijuu or other entity thinking

 **Taijuu Kage Bunshin no Jutsu-** Justus or other techniques

"Vengeance can change a person. Turn you into something you never thought you were capable of becoming."\- Flashback

* * *

 **QNA**

 **None**

"Nagato!"

The frantic, yet stern shout came from Konan. She couldn't believe her eyes. How had Naruto not only manage to overpower Nagato's hold on him, but so effortlessly dispatch her as well. She had let her guard down for a second, and that mistake cost her dearly. But she couldn't afford to sit idly as multiple shinobi had just entered the tree.

The konoha nin entered the tree with haste after they felt the brief flare of chakra. Cat and her squad, along with inochi, noticed the fragile looking man that was being dealt with by Naruto. It seemed that he had managed to take out the leader after all. With that threat taken care of, that left only one more enemy to deal with. A silent agreement was shared between them and they approached the laying kunochi before them.

Konan acted quickly and recovered from her prone position. Sidestepping a slash from a tanto being welded by a badger masked ANBU, she grabbed the man by the wrist and hurled him over her shoulder, and into the path of another oncoming shinobi, with considerable force. The two shinobi burst into smoke and were replaced by logs.

 _'Substitution!'_

She had only seconds to conjure up a paper dome strong enough to stop the kunai heading towards her from multiple directions.

 _'This is not good,'_ thought Konan within the confines of her barrier. She hadn't had the chance to see what became of Nagato and Naruto before the assault on her started. Growing worried, she willed a small opening to form in the direction she knew the two Uzumakis were.

She took a quick glance at Nagato. His body was blocked by an unmoving Naruto, a small cloak of chakra still around him. It felt similar, but yet different. The chakra rod was still in his stomach. But Nagatos own wound was unseen by her, as well as the thick crimson and yellow chakra moving between the two rods.

 _'Did Nagato regain control again? Why hasn't he fought back yet?'_

Upon closer inspection, she could see that Nagato was whispering something to the blond. What that may be, she could not tell, but she did take note of something. Nagato looked weak. Much weaker then he usually did. His already pale skin looked much whiter than what she remembered, and his movements looked strained. In that moment, she witnessed the hand he was using to support himself fall limp, and his head lean on the jinchuriki's shoulder. But what had frightened her the most were his unblinking eyes seemingly focused on nothing.

The dome around her shot in every direction, flinging the embedded kunai and sharpened paper towards her attackers. The ANBU sought shelter behind earth jutsus and replacement techniques. The entire tree seemed to come to life. piece after piece started to fall off of it and started to spin around the female akatsuki as if an unseen hurricane had taken form around her. Soon enough, their vision were obstructed by the countless sheets that made up the tree.

With cold calculation, Konan moved swiftly and with purpose towards her friend. She punched the blond with unrestrained power, and sent him in the direction she had just come from. Grabbing Nagato, Konan sprouted paper wings and took to the skies before Naruto could recover and intercept her. She looked like a white blur in the sky, leaving the paper tornado behind to hide her escape. She had pumped all the chakra she could into her escape plan, leaving just enough to aid her flight back to Ame.

Unbeknown to her, Naruto never moved, not even to shield himself from the sharp paper flying in all directions. The rod in his abdomen was still glowing with the yin and yang chakra the kyuubi had used earlier.

* * *

Naruto had endured much in his 18 years of life. He was no stranger to pain. He has been stabbed by kunai, sliced by shuriken, and pummeled by jutsus. He had even been impaled by his so called brother when trying to bring him back to the village so many years ago. Emotional pain was no exception either. He was born an orphan, no clue as to who his parents may be. He didn't know a parents love. To make matters worse, he had become a scapegoat for the village growing up. No one wanted to associate with him. People spat at him and treated him like the plague itself, and he had no idea why at the time. Some even got physical, but nothing more than some forceful shoves or a random item being lodged his way. The resentment and neglect had hurt him the most, but like any wound, he powered through it.

But what he felt now could not compare.

 _"What is this? What is going on?"_

Before him, Naruto was seeing things he could not comprehend.

He saw multiple random flashes. Mostly images of a war torn and constantly raining place. Things were flashing fast, but he could still see and understand what was going on. But what shocked him the most was that he could feel something as well. He recalled seeing a redheaded woman struggling with some shinobi wearing leaf headbands.

"Run Nagato!" she yelled

Naruto saw the woman get killed by the shinobi, and felt sadness and rage.

Next thing he sees is the bodies of the shinobi laying on the floor, and he recalls feeling fear and regret.

The images continue racing through his mind.

He sees the time when he met and befriended an orange haired boy, and a blue haired girl.

He recalls when a snake like man, a busty blond, and a white haired man saved him and the resulting training he and his small family had received from the white haired man.

 _"Is that…"_

Naruto didn't finish that thought as he continued to experience emotions to these memories that he has never seen before.

Defeating Hanzo, the creation of Akatsuki, rebuilding Ame, killing Yahiko, Meeting Tobi. The memories continued to bombard him along with the appropriate emotions.

Then came the attack on konoha. He remembered killing countless leaf shinobi and civilians. Kakashi, Shizune, Hinata. But one death had shook him to the core.

* * *

Naruto looked at Nagato's outstretched hand lifting the woman before him with a chakra rod in the other. 

"You will tell me where he is." came the stock voice of Pein.

"Go… to hell." came the choked reply from the woman.

 _'No.'_ thought Naruto.

Without hesitation, Nagato plunged the rod into her stomach and let her drop to her knees. She yelled out in pain, clutching her stomach, almost cradling her wound. Large tears left her eyes, but she remained looking down towards her stomach.

 _'No… kami, please don't!'_ thought Naruto. He tried in vain to let go of the weapon in his hand but nothing happened. Tears began forming in his eyes.

"Ba…Bastard."

"Tell me, and i shall let you live."

She remained impassive. Her wound wasn't fatal, at least not yet, but the damage had been done. 

"Very well then."

Pein looked on as another figure appeared behind the woman. He had hoped to get the information before his Human path had arrived, but alas, that wasn't meant to be. The Human path had gotten a lead as to who may know the jinchurikis whereabouts from a short haired medic nin. She had been the Hokage's assistant and was the one to examine the previous animal path. Unfortunately, she didn't know the whereabouts of the blond, but knew of someone who did. Deva path had been the first to find the woman.

The Human Path grabbed the top of the woman head rather harshly. She looked into the eyes of Deva path and whispered to herself, before closing her eyes.

Naruto tried in vain to stop the Human path from doing what he did to Shizune, but nothing happened. He fixed his gaze at the woman before him. Her words were soft, but Naruto heard them clear as day.

"Im sorry, Naruto-koi."

* * *

Her body hit the ground with a soft thud. All noise around him seemed to stop, or maybe he just stopped paying attention. Memories kept flashing before him but he didn't care. He remembered only her. Her memories flashed before him. All the time they spent together, every moment, every kiss, every time they made love. Everything flashed before him, causing him more pain with every passing moment, like a knife slowly making its way to his heart. He hurt. Nothing compared to what he felt right now.

With a bone chilling yell, Naruto exploded into a crimson shower of chakra. The maelstrom of paper dissipated instantly with the violent explosion. The ANBU nearby had been blown away as well. The turn of events had shocked them. The run away Akatsuki were no longer on their minds as now they had a much bigger problem. Before them was an 8-tailed Naruto ready to lay waste to his surroundings.

Looking down, Naruto yanked out the rod before crushing it in his hand and throwing them down. A sudden noise drew his attention from black shards at his feet. Inochi Yamanaka was struggling to get up. In his struggles, he had unknowingly attracted the jinchurikis full attention. Naruto sent all 8 tails towards his new target. Inochi, still dazed by the knockback, could do nothing but raise his hands in defense.

Splinters littered his face and a blue light shone through his closed eyes. Opening his eyes, he saw a mangled piece of wood snaking around several tails. The wood managed to stop 7 of the tails, but one was mere inches from his face, still struggling to move. A blue tendril seemed to be restraining the appendage. Following the tendril, he noted that it was originating from a blue crystal attached to a necklace laying right next to his foot.

"That could have ended badly", came a voice from behind him.

He turned around to see Yamato crouching on the ground, with his hands flat against the dirt, presumably to call forth the shield that just saved his life.

"We need to subdue Naruto, but i cant do it alone! Quickly, get that necklace back on him!" yelled Yamato.

Yamato pumped more chakra into his attack and the wood quickly began to encircle the tails individually, before making their way towards naruto himself. They twisted and turned around him, only barley managing to contain him. 5 of the tails broke free and began swinging wildly, trying to do as much damage as possible. Naruto however remained encased by the wood.

"Necklace! Now!"

Not needing to be told a third time, Inochi bent down and grabbed the Necklace. Dodging the deadly tails, he managed to get near before a newly freed tail knocked him back a couple feet.

The tail was about to continue its assault before three black shadows creeped onto various tails, including the one that was intent on striking him. Shikaku along with two other Naras were doing their best to subdue three more tails.

"Right… On time…" Said a struggling Shikaku.

With that taken care of, Inochi continued on and placed the necklace around the kyuubified Naruto's neck. Immediately, Blue light started to encase and attack Naruto. Despite all of this, Naruto kept thrashing about.

"Its… Not… Working", said Shikaku.

"Naruto's not… fighting against… the kyuubi. We need him… to cooperate." groaned Yamato.

Inochi thought for a moment. He knew that there was only one way they were going to get Naruto's attention. Without hesitation, he began his jutsu.

 **"Mind Transfer Jutsu."**

* * *

Inochi looked at his surroundings. Greeting him was a sewer-like place. On the far end was a giant cage, with red chakra leeching out of it and into a kneeling Naruto. Seemingly oblivious to all around him, Naruto just allowed the chakra to do as it pleased. Inochi ran up to him, wary of the cage, knowing whats behind it.

"Naruto! Naruto wake up!"

No answer.

"Naruto!"

" **Its no use."** came a voice behind Inochi.

" **Soon, this seal will weaken, and i will be free. So run while you still can"**

Looking back down at the blond, Inochi decided to do something he was morally against. invading a fellow leaf nin's memories. If he could shift through them, maybe he could bring forth the most pleasant and knock some sense into Naruto.

"Im sorry Naruto, but we need you right now."

With that, Inochi began searching.

* * *

The thrashing suddenly stopped. He had put up one hell of a fight, but Naruto had finally stopped moving. His tails began to shrink and his cloak began to fade as he fell to his knees.

"Did…it work." The voice came from a panting Shikaku.

"I think so"answered Yamato.

A sigh of relief escaped from the two men as they looked at the calming Naruto.

"That was really reckless Inochi, you could have been hurt in his mindscape. What were you thinking Inochi." asked Shikaku without turning back.

No response.

"Inochi?"

Now worried, they looked towards Inochi. He was sitting on the ground with his back away from them and his head laying low. They began to walk towards him, but were halted on the spot by the mind walker.

"Are you o…"

"Im fine. Really. Just… just check up on Naruto for me ok." interrupted the Yamanaka, genuine worry on his face for his fellow blond.

Startled by the response, they nonetheless obliged when they noticed his worry for the jinchuriki. They turned their focus back to Naruto, intent on checking over the kneeling blond. But what they saw had caught them off guard.

Naruto lifted his head, his eyes focused on the pair before him. Tears seemed to be running down his cheek but his face was duo focused on his eyes. His gaze looked empty, as if all life and joy had been sucked out of them. Fatigue over took Naruto and he began slumping towards his side. He fell with a light thud, sleep finally taking hold of him.

Shikaku and Yamato remained still. No movement was made to assist the blond as something else had grasped their complete attention. The shinobi kept their silence for a while, both pondering the implications of the scene they had just witnessed.

Finally, they spoke up.

"But thats… thats imposible."

"It can't be. He shouldn't…"

The three men remained still, trying to ascertain if what they saw was real. It had to be an illusion. After all, the three men could have sworn that for a split second, they saw a pair of red eyes, with three tomoe in each, staring back.

* * *

 **Dont have much to say. Sorry about the unannounced hiatus. Couldn't figure out how to write this chapter and i sorta just lost interest after rewriting it a couple times. You'd think that after a year, i'd have more than this measly chapter but apparently not. Still not sure how often i will update. I will try to avoid year long waiting times but I'm no writer. Thanks for sticking with me guys.**

 **Till next time.**


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